GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucO in Pseudomonas fluorescens FW300-N2C3

Align NADH-dependent aldehyde reductase (EC 1.1.1.77; EC 1.1.1.244; EC 1.1.1.1) (characterized)
to candidate AO356_25665 AO356_25665 3-beta hydroxysteroid dehydrogenase

Query= metacyc::G3O-32155-MONOMER
         (298 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_25665
          Length = 288

 Score =  218 bits (554), Expect = 2e-61
 Identities = 121/291 (41%), Positives = 174/291 (59%), Gaps = 11/291 (3%)

Query: 1   MKVFITGASGFIGSAVLSELISSGHEVVGLARSDEAAAKIKSIDPAAKILRGDLKDLEIL 60
           M VF+TGA+G++G++V+ +LI++GH V GLAR +E  A + +    AK++ G L DLEIL
Sbjct: 1   MHVFVTGATGWVGASVVQDLIAAGHRVTGLARCEEKGATLAAT--GAKVIPGTLDDLEIL 58

Query: 61  KKGATESDGVIHLGFVHDFKNFEQCCEIDRQATVAMLESLKGSNKPFLYTNGTLSLRPNK 120
              A+ +D VIH  F HDF  F +  + DR+A   + ++L+GS++P L T+G   L   +
Sbjct: 59  HSAASAADAVIHTAFNHDFSRFAENAQQDRRAIETLGDALRGSDRPLLVTSGLFGL--TR 116

Query: 121 VANEQDGIDEDSKILRAVTEQVALSYKDKGVSARIVRLPFSVHGKGDKAFVPILMNIAKA 180
            A+E + +   S      +E  A    ++G     VRL  SVHG GD  FVPIL+ +A+ 
Sbjct: 117 GASELEVVSPASP---RKSEAAARDLAERGGRVATVRLAPSVHGLGDHGFVPILIRLARQ 173

Query: 181 AGKSGYVGQGTNAWAAVHRLDTAPLFRLVLEKGKTGQVYHCVGEQGIPFKDIARVIGEIL 240
           +G S Y G G++ W+ VHR D A ++RL LE+G T  VYH V ++ +PFKDIA+ IG  L
Sbjct: 174 SGVSAYPGDGSHCWSGVHRQDAARVYRLALEQGVTQSVYHAVADEAVPFKDIAQAIGRGL 233

Query: 241 NVPVASIPVDDAESHFGFLTCFVTRDGPVSSEGTRKELGWQPQQIGLLEDI 291
            +PV S        HFG+       +  VSSE TR  LGW P   GLL+D+
Sbjct: 234 GLPVES----REREHFGWFAHMAGANMAVSSEYTRALLGWTPSGPGLLDDL 280


Lambda     K      H
   0.318    0.136    0.393 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 242
Number of extensions: 11
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 298
Length of database: 288
Length adjustment: 26
Effective length of query: 272
Effective length of database: 262
Effective search space:    71264
Effective search space used:    71264
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory